Third quarter net profit slumped 10.1 percent from a year earlier to €249 million, the maker of Aspirin said in a statement.
Sales fell 7.0 percent to €7.39 billion in the three months to September, it added.
Analysts polled by Dow Jones Newswires had forecast a 10 percent increase in net profit and a fall of five percent in sales.
"We are still adhering to our ambitious full-year forecast for the Bayer group," chairman Werner Wenning said in a statement."We still expect to post full-year group sales of between 31 billion and 32 billion euros.”
In the third quarter, core earnings before interest and tax (EBIT) fell 6.1 percent to €837 million.
The group's three main divisions showed varying fortunes, with HealthCare posting a sales increase of 3.5 percent to €3.94 billion owing to strong sales of the cancer drug Nexavar and heart attack treatment Aspirin Cardio.
Levitra, a treatment for erectile dysfunction also sold particularly well, the company said.
Earnings at Bayer's MaterialScience division, which produces high-tech materials for construction, were much better than in the second quarter, and at €238 million almost reached the year earlier level, the company said.
Year-on-year, however, sales were down 20 percent at €2 billion.
The weakest results were turned in by the CropScience division, which produces fertilizers and other products for the agricultural sector and which had helped support the group's overall earnings until this quarter.
Sales there were down 8.7 percent at €1.14 billion, owing to "lower prices for key crop commodities, adverse weather conditions and higher trade inventories of crop protection products," Wenning said.
Bayer's debt stood at €10.7 billion as of September 30, a decline of €1 billion from the previous quarter.
The group expected to take charges of €350 million in connection with restructuring programmes by the end of the year but Wenning was upbeat about the near- to medium-term prospects.
"In light of the portfolio realignment we have undertaken in recent years, we are confident about the ongoing development of our enterprise in the coming quarters," he said.